I am looking for a software with which I can represent my multiple sequence alignment results in a more concise representative block diagram, which could show the relative conservation of residues among the various sets of sequences. Please let me know if you have some idea about this. Thanks.
I don't know if you mean, like a tree with the conserved zones, a program Like Clustalw or X create that representation as a way of calculate the scores of the alignment matrix. you only ask for sohw tree. Vector NTi shows the tree in every alignment.
Hi Ranjan
In my opinion you should use a software like adobe illustartor or coral draw to make such representations. I actually use these programs for making such block diagrams/line diagrams
Hi Ajay, I would like the color of the blocks to be exactly proportional to the length of conservtation/domain of amino acid sequence.
This might not relate to the example picture you posted, but upon reading your question, I immediately thought of Weblogo (http://weblogo.threeplusone.com/). To get the kind of diagrams you posted in a more automatic manner, you might want to script it in R or Perl (using the GD module, for example).
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